If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ), 'gf_id' => 'HOM05D001142', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001142' ), 'data_identifier' => 'HOM05D001142', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001142', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30350' => 'bna', 'A04p26050' => 'bna', 'A06p45640' => 'bna', 'A07p45510' => 'bna', 'A09p22560' => 'bna', 'Aa31LG4G190' => 'aar', 'Aa31LG9G6080' => 'aar', 'Aa31sc652G100' => 'aar', 'Aa31sc652G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2530' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1202' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2551' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1936' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2564' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.299' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.562' => 'aag', 'Actinidia05648' => 'ach', 'Actinidia07590' => 'ach', 'Actinidia08981' => 'ach', 'Actinidia09213' => 'ach', 'Actinidia16563' => 'ach', 'Actinidia24751' => 'ach', 'Ah.01g021440' => 'amhyb', 'Ah.07g200330' => 'amhyb', 'Ah.12g055010' => 'amhyb', 'Ah.14g089620' => 'amhyb', 'AL2G41660' => 'aly', 'AL4G29590' => 'aly', 'AL8G11520' => 'aly', 'Aqoxy3G02359' => 'aox', 'Aqoxy3G02364' => 'aox', 'Aqoxy4G00719' => 'aox', 'Aqoxy7G01682' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5D55UE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G9G3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL7XSL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FLA5DV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3H6Y6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69ZU5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2ZPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK5IQF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR4FGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1YKNW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD6HKD' => 'arhy', 'AT1G79900' => 'ath', 'AT2G33820' => 'ath', 'AT5G46800' => 'ath', 'ATR0057G112' => 'atr', 'ATR0580G085' => 'atr', 'ATR0752G004' => 'atr', 'ATR0916G008' => 'atr', 'Atru.chr1.3303' => 'acertr', 'Atru.chr10.1824' => 'acertr', 'Atru.chr10.1826' => 'acertr', 'Atru.chr10.1841' => 'acertr', 'Atru.chr6.1714' => 'acertr', 'AUR62007287' => 'cqu', 'AUR62014847' => 'cqu', 'AUR62014848' => 'cqu', 'AUR62016457' => 'cqu', 'AUR62017043' => 'cqu', 'AUR62018719' => 'cqu', 'AUR62042931' => 'cqu', 'BcaB07g30819' => 'bca', 'BcaC01g05823' => 'bca', 'BcaC02g07765' => 'bca', 'BcaC02g07766' => 'bca', 'BcaC03g16891' => 'bca', 'BcaC04g21680' => 'bca', 'BcaC06g31442' => 'bca', 'BcaC06g34345' => 'bca', 'BcaC08g47559' => 'bca', 'BolC2t10821H' => 'bol', 'BolC3t14589H' => 'bol', 'BolC6t40445H' => 'bol', 'BolC7t43552H' => 'bol', 'BolC9t55753H' => 'bol', 'BraA02t08050Z' => 'bra', 'BraA04t18107Z' => 'bra', 'BraA06t27433Z' => 'bra', 'BraA07t32053Z' => 'bra', 'BraA09t37862Z' => 'bra', 'C02p47880' => 'bna', 'C03p22050' => 'bna', 'C04p63390' => 'bna', 'C06p54340' => 'bna', 'C07p30120' => 'bna', 'C09p28910' => 'bna', 'CAN.G100.75' => 'can', 'CAN.G201.26' => 'can', 'CAN.G313.7' => 'can', 'CAN.G395.11' => 'can', 'CAN.G438.76' => 'can', 'CAN.G641.34' => 'can', 'CANSAT11G1440' => 'cansat', 'CANSAT21G2582' => 'cansat', 'CANSAT56G1000' => 'cansat', 'CARHR074590' => 'chi', 'CARHR127920' => 'chi', 'CARHR174680' => 'chi', 'Carub.0002s2760' => 'cru', 'Carub.0004s1549' => 'cru', 'Carub.0008s0111' => 'cru', 'Ca_06076_v3' => 'car', 'Ca_18574_v3' => 'car', 'Ca_20384_v3' => 'car', 'Ca_22638_v3' => 'car', 'CBR_g21058' => 'cbr', 'CBR_g34686' => 'cbr', 'Cc02_g13610' => 'ccan', 'Cc02_g13620' => 'ccan', 'Cc04_g03240' => 'ccan', 'Cc09_g09300' => 'ccan', 'CDE02G4080' => 'cde', 'CDE05G3542' => 'cde', 'CDE06G1818' => 'cde', 'CDE11G0793' => 'cde', 'Cfa000507' => 'cfa', 'Cfa002079' => 'cfa', 'Cfa012433' => 'cfa', 'Cfa012435' => 'cfa', 'Cfa022525' => 'cfa', 'Cfa025208' => 'cfa', 'Ciclev10012332m.g' => 'ccl', 'Ciclev10016062m.g' => 'ccl', 'Ciclev10026140m.g' => 'ccl', 'CiPaw.01G238000' => 'cil', 'CiPaw.02G150400' => 'cil', 'CiPaw.09G062000' => 'cil', 'CiPaw.11G092800' => 'cil', 'CiPaw.12G063400' => 'cil', 'ClCG03G008100' => 'cla', 'ClCG07G013100' => 'cla', 'ClCG09G002070' => 'cla', 'ClCG09G011950' => 'cla', 'ClCG09G011960' => 'cla', 'ClCG10G001630' => 'cla', 'COL.COLO4_17040' => 'col', 'COL.COLO4_30396' => 'col', 'COL.COLO4_31439' => 'col', 'Cpa.g.c28192.2' => 'cpa', 'Cpa.g.sc27.41' => 'cpa', 'Cpa.g.sc71.59' => 'cpa', 'Cre04.g222750' => 'cre', 'Cre04.g223300' => 'cre', 'Cre06.g295400' => 'cre', 'Cre16.g683259' => 'cre', 'Cre17.g747797' => 'cre', 'CsaV3_1G012450' => 'csa', 'CsaV3_3G001750' => 'csa', 'CsaV3_3G025070' => 'csa', 'CsaV3_3G049210' => 'csa', 'CsaV3_3G049220' => 'csa', 'CsaV3_7G033250' => 'csa', 'CSS0010488' => 'camsi', 'CSS0016592' => 'camsi', 'CSS0017599' => 'camsi', 'CSS0023163' => 'camsi', 'CSS0028967' => 'camsi', 'CSS0029517' => 'camsi', 'CSS0034183' => 'camsi', 'CSS0035709' => 'camsi', 'CSS0037262' => 'camsi', 'CSS0038304' => 'camsi', 'CSS0044536' => 'camsi', 'DCAR_005627' => 'dca', 'DCAR_008273' => 'dca', 'DCAR_016218' => 'dca', 'DCAR_024965' => 'dca', 'DCAR_028059' => 'dca', 'DCAR_031775' => 'dca', 'Dinv17332' => 'din', 'Dinv30500' => 'din', 'Dinv38037' => 'din', 'Dinv40584' => 'din', 'Duzib068G1296' => 'dzi', 'Duzib084G0367' => 'dzi', 'Duzib192G0392' => 'dzi', 'Duzib205G0166' => 'dzi', 'Duzib235G1012' => 'dzi', 'Duzib235G1209' => 'dzi', 'ECA232G4740' => 'eca', 'ECA240G3457' => 'eca', 'ECA246G1249' => 'eca', 'ECA246G2988' => 'eca', 'ECA247G1523' => 'eca', 'ECA248G1175' => 'eca', 'EL10Ac5g12126' => 'bvu', 'EL10Ac8g20417' => 'bvu', 'EL10Ac9g22009' => 'bvu', 'EL10Ac9g22013' => 'bvu', 'Eucgr.E00280' => 'egr', 'Eucgr.E03259' => 'egr', 'Eucgr.F03022' => 'egr', 'Eucgr.J02981' => 'egr', 'FAN01G1552' => 'fan', 'FAN02G0320' => 'fan', 'FAN02G0525' => 'fan', 'FAN02G0679' => 'fan', 'FAN02G1537' => 'fan', 'FAN02G4381' => 'fan', 'FAN03G0269' => 'fan', 'FAN05G2303' => 'fan', 'FAN05G4599' => 'fan', 'FAN06G5013' => 'fan', 'FAN09G1739' => 'fan', 'FAN09G4855' => 'fan', 'FAN10G3996' => 'fan', 'FAN11G3542' => 'fan', 'FAN14G2859' => 'fan', 'FAN16G1027' => 'fan', 'FAN21G1523' => 'fan', 'FAN25G0831' => 'fan', 'FvH4_3g08870' => 'fve', 'FvH4_6g31430' => 'fve', 'FvH4_6g31440' => 'fve', 'FvH4_7g06810' => 'fve', 'Glyma.01G019000' => 'gma', 'Glyma.01G097100' => 'gma', 'Glyma.02G069300' => 'gma', 'Glyma.03G038000' => 'gma', 'Glyma.03G083600' => 'gma', 'Glyma.04G143500' => 'gma', 'Glyma.07G005300' => 'gma', 'Glyma.07G199200' => 'gma', 'Glyma.08G205800' => 'gma', 'Glyma.08G272600' => 'gma', 'Glyma.09G203900' => 'gma', 'Glyma.13G177267' => 'gma', 'Glyma.13G177333' => 'gma', 'Glyma.13G358800' => 'gma', 'Glyma.15G015200' => 'gma', 'Gohir.A03G001300' => 'ghi', 'Gohir.A05G159700' => 'ghi', 'Gohir.A09G082400' => 'ghi', 'Gohir.A10G080300' => 'ghi', 'Gohir.A11G030400' => 'ghi', 'Gohir.A12G208500' => 'ghi', 'Gohir.D03G170966' => 'ghi', 'Gohir.D05G162400' => 'ghi', 'Gohir.D06G133450' => 'ghi', 'Gohir.D09G082200' => 'ghi', 'Gohir.D10G071000' => 'ghi', 'Gohir.D11G029000' => 'ghi', 'Gohir.D12G211100' => 'ghi', 'Gorai.003G181500' => 'gra', 'Gorai.006G098000' => 'gra', 'Gorai.007G031700' => 'gra', 'Gorai.008G226600' => 'gra', 'Gorai.009G167400' => 'gra', 'Gorai.010G155300' => 'gra', 'Gorai.011G075400' => 'gra', 'GSVIVG01013163001' => 'vvi', 'GSVIVG01017089001' => 'vvi', 'GSVIVG01021089001' => 'vvi', 'HanXRQChr01g0004661' => 'han', 'HanXRQChr03g0083971' => 'han', 'HanXRQChr04g0096091' => 'han', 'HanXRQChr04g0110761' => 'han', 'HanXRQChr04g0110771' => 'han', 'HanXRQChr04g0119611' => 'han', 'HanXRQChr05g0138541' => 'han', 'HanXRQChr05g0138551' => 'han', 'HanXRQChr06g0166041' => 'han', 'HanXRQChr06g0166051' => 'han', 'HanXRQChr06g0167461' => 'han', 'HanXRQChr09g0275191' => 'han', 'HanXRQChr13g0414141' => 'han', 'HanXRQChr14g0438231' => 'han', 'HanXRQChr17g0535811' => 'han', 'HanXRQChr17g0547471' => 'han', 'HanXRQChr17g0547481' => 'han', 'Haze_08243' => 'cav', 'Haze_16400' => 'cav', 'Haze_27345' => 'cav', 'Hma1.2p1_0991F.1_g245110' => 'hma', 'Hma1.2p1_1455F.1_g284490' => 'hma', 'HPP92_014618' => 'vpl', 'HPP92_017548' => 'vpl', 'HPP92_022443' => 'vpl', 'Hund00631' => 'sun', 'Hund14400' => 'sun', 'Hund21213' => 'sun', 'Hund23777' => 'sun', 'Lalb_Chr04g0262761' => 'lal', 'Lalb_Chr05g0216131' => 'lal', 'Lalb_Chr05g0228881' => 'lal', 'Lalb_Chr09g0325711' => 'lal', 'Lalb_Chr09g0327741' => 'lal', 'Lalb_Chr09g0327751' => 'lal', 'Lalb_Chr16g0392041' => 'lal', 'Lalb_Chr24g0395861' => 'lal', 'Lj1C1202G13' => 'lonja', 'Lj2A240T32' => 'lonja', 'Lj2g0016670' => 'lja', 'Lj2g0023038' => 'lja', 'Lj3g0006788' => 'lja', 'Lj3g0007103' => 'lja', 'Lj3g0012112' => 'lja', 'Lj3g0015708' => 'lja', 'Lj3g0017049' => 'lja', 'Lj4g0020774' => 'lja', 'Lj4g0022253' => 'lja', 'Lj5A59G64' => 'lonja', 'Lj8A300T30' => 'lonja', 'Lsat_1_v5_gn_1_128461' => 'lsa', 'Lsat_1_v5_gn_1_35200' => 'lsa', 'Lsat_1_v5_gn_2_100200' => 'lsa', 'Lsat_1_v5_gn_3_17700' => 'lsa', 'Lsat_1_v5_gn_4_102201' => 'lsa', 'Lsat_1_v5_gn_6_79421' => 'lsa', 'Manes.04G124700' => 'mes', 'Manes.11G045200' => 'mes', 'Manes.15G182000' => 'mes', 'Manes.17G013300' => 'mes', 'Manes.17G047600' => 'mes', 'Mapoly0001s0527' => 'mpo', 'Mapoly0051s0030' => 'mpo', 'Mapoly0076s0008' => 'mpo', 'MBI01_g41481_MAGBIO' => 'mbi', 'MBI02_g32443_MAGBIO' => 'mbi', 'MBI04_g19384_MAGBIO' => 'mbi', 'MBI04_g22929_MAGBIO' => 'mbi', 'MCO01G595' => 'mco', 'MCO02G507' => 'mco', 'MCO03G515' => 'mco', 'MCO07G218' => 'mco', 'MCO07G604' => 'mco', 'MD05G1312200' => 'mdo', 'MD06G1033900' => 'mdo', 'MD09G1211700' => 'mdo', 'MD10G1291700' => 'mdo', 'MD16G1274700' => 'mdo', 'MD17G1194000' => 'mdo', 'Medtr2g102010' => 'mtr', 'Medtr4g012850' => 'mtr', 'Medtr4g088545' => 'mtr', 'Medtr5g030530' => 'mtr', 'Medtr8g066975' => 'mtr', 'MELO3C002619.2' => 'cme', 'MELO3C003405.2' => 'cme', 'MELO3C003406.2' => 'cme', 'MELO3C003407.2' => 'cme', 'MELO3C012965.2' => 'cme', 'MELO3C013855.2' => 'cme', 'MELO3C024239.2' => 'cme', 'Migut.D01025' => 'egut', 'Migut.I00883' => 'egut', 'Migut.K00898' => 'egut', 'Migut.M01123' => 'egut', 'MSTRG.11069' => 'ama', 'MSTRG.15674' => 'ama', 'MSTRG.15869' => 'ama', 'MSTRG.3715' => 'ama', 'MSTRG.9458' => 'ama', 'Nitab4.5_0000082g0460' => 'nta', 'Nitab4.5_0000256g0400' => 'nta', 'Nitab4.5_0000351g0090' => 'nta', 'Nitab4.5_0001249g0020' => 'nta', 'Nitab4.5_0001249g0030' => 'nta', 'Nitab4.5_0002308g0070' => 'nta', 'Nitab4.5_0002308g0080' => 'nta', 'Nitab4.5_0002903g0020' => 'nta', 'Nitab4.5_0003348g0040' => 'nta', 'Nitab4.5_0003351g0050' => 'nta', 'Nitab4.5_0003942g0080' => 'nta', 'Nitab4.5_0018389g0020' => 'nta', 'Nn1g03646' => 'nnu', 'Nn1g04160' => 'nnu', 'Nn1g06466' => 'nnu', 'Nn1g08049' => 'nnu', 'Nn2g11752' => 'nnu', 'Nn3g19185' => 'nnu', 'Nn6g34509' => 'nnu', 'Nn8g39188' => 'nnu', 'Oeu000453.1' => 'oeu', 'Oeu012256.1' => 'oeu', 'Oeu024067.1' => 'oeu', 'Oeu029363.1' => 'oeu', 'Oeu030319.1' => 'oeu', 'Oeu032325.1' => 'oeu', 'Os01g0225000' => 'osa', 'Os10g0573700' => 'osa', 'Os10g0573800' => 'osa', 'Os11g0423800' => 'osa', 'Peaxi162Scf00015g00448' => 'pax', 'Peaxi162Scf00130g00111' => 'pax', 'Peaxi162Scf00207g00941' => 'pax', 'Peaxi162Scf00615g00519' => 'pax', 'Peaxi162Scf01100g00112' => 'pax', 'PGR042G2735' => 'pgr', 'PGR042G3261' => 'pgr', 'PGR102G3277' => 'pgr', 'PGSC0003DMG400002099' => 'stu', 'PGSC0003DMG400007617' => 'stu', 'PGSC0003DMG400008144' => 'stu', 'PGSC0003DMG400016535' => 'stu', 'PGSC0003DMG400029730' => 'stu', 'PGSC0003DMG401005606' => 'stu', 'Phvul.002G142100' => 'pvu', 'Phvul.002G230400' => 'pvu', 'Phvul.003G285400' => 'pvu', 'Phvul.005G167800' => 'pvu', 'Phvul.010G149800' => 'pvu', 'Potri.001G142600' => 'ptr', 'Potri.001G182000' => 'ptr', 'Potri.003G053900' => 'ptr', 'Potri.003G091500' => 'ptr', 'Potri.004G046801' => 'ptr', 'Potri.011G056000' => 'ptr', 'Pp3c15_17210' => 'ppa', 'Pp3c18_6190' => 'ppa', 'Pp3c1_42820' => 'ppa', 'Pp3c20_15390' => 'ppa', 'Pp3c21_17980' => 'ppa', 'Pp3c21_9970' => 'ppa', 'Pp3c22_3240' => 'ppa', 'Pp3c7_11870' => 'ppa', 'PRCOL_00000422' => 'pco', 'PRCOL_00003229' => 'pco', 'PRCOL_00003406' => 'pco', 'PRCOL_00004723' => 'pco', 'PRCOL_00006759' => 'pco', 'Prupe.3G069600' => 'ppe', 'Prupe.3G069700' => 'ppe', 'Prupe.4G050500' => 'ppe', 'Prupe.8G063200' => 'ppe', 'Psat0s2998g0040' => 'psa', 'Psat2g136080' => 'psa', 'Psat4g120840' => 'psa', 'Psat7g115000' => 'psa', 'Psat7g251200' => 'psa', 'PSO063G2045' => 'pso', 'PSO063G2835' => 'pso', 'PSO210G3040' => 'pso', 'PSO782G1702' => 'pso', 'PSO782G1802' => 'pso', 'PSO832G4555' => 'pso', 'QL05p022726' => 'qlo', 'QL05p022739' => 'qlo', 'QL05p041636' => 'qlo', 'QL12p005464' => 'qlo', 'RcHm_v2.0_Chr2g0138231' => 'rch', 'RcHm_v2.0_Chr2g0138241' => 'rch', 'RcHm_v2.0_Chr5g0008881' => 'rch', 'RcHm_v2.0_Chr7g0209661' => 'rch', 'Rhsim06G0121900' => 'rsi', 'Rhsim12G0198700' => 'rsi', 'Rhsim13G0179700' => 'rsi', 'Sabra01G0111400' => 'sbr', 'Sabra01G0145500' => 'sbr', 'Sabra03G0061200' => 'sbr', 'Sabra04G0029200' => 'sbr', 'SalBow2G0085' => 'sbo', 'SalBow2G3458' => 'sbo', 'SalBow3G2134' => 'sbo', 'SalBow5G2069' => 'sbo', 'SalBow5G3303' => 'sbo', 'SalBow6G5352' => 'sbo', 'SalBow8G2584' => 'sbo', 'SalBow8G4316' => 'sbo', 'Sc01g0007460' => 'sci', 'Sc12g0009340' => 'sci', 'Sc17g0006090' => 'sci', 'Sed0001190' => 'sed', 'Sed0010416' => 'sed', 'Sed0014002' => 'sed', 'Sed0015572' => 'sed', 'Sed0016744' => 'sed', 'Sed0019488' => 'sed', 'Sed0024308' => 'sed', 'Sed0024625' => 'sed', 'SEGI_16121' => 'sgi', 'SEGI_29281' => 'sgi', 'SEGI_33540' => 'sgi', 'SEGI_34588' => 'sgi', 'SGA_v2.0_scaffold22G09685' => 'sas', 'SGA_v2.0_scaffold45G17185' => 'sas', 'SGA_v2.0_scaffold5G02568' => 'sas', 'SHI01675' => 'shi', 'SHI10943' => 'shi', 'SHI53762' => 'shi', 'SMO174G0187' => 'smo', 'SMO269G0016' => 'smo', 'SMO356G0048' => 'smo', 'Solyc02g077910.4' => 'sly', 'Solyc03g120100.3' => 'sly', 'Solyc06g061170.3' => 'sly', 'Solyc06g066680.3' => 'sly', 'Solyc10g009090.3' => 'sly', 'Solyc10g079200.2' => 'sly', 'Sopen02g022760' => 'spe', 'Sopen03g038970' => 'spe', 'Sopen06g021370' => 'spe', 'Sopen06g024960' => 'spe', 'Sopen10g004870' => 'spe', 'Sopen10g029850' => 'spe', 'Sp2g11620' => 'spa', 'Sp4g16210' => 'spa', 'Sp5g35870' => 'spa', 'TAR375G0658' => 'tar', 'TAR375G0894' => 'tar', 'TAR626G0335' => 'tar', 'TAR626G1946' => 'tar', 'TAR629G1011' => 'tar', 'THA.LOC104800428' => 'tha', 'THA.LOC104812827' => 'tha', 'THA.LOC104820555' => 'tha', 'THA.LOC104827762' => 'tha', 'Thecc.03G228200' => 'tca', 'Thecc.06G090000' => 'tca', 'Thecc.06G183800' => 'tca', 'Thhalv10000972m.g' => 'esa', 'Thhalv10016989m.g' => 'esa', 'Thhalv10018951m.g' => 'esa', 'TPR.G1034' => 'tpr', 'TPR.G14898' => 'tpr', 'TPR.G15270' => 'tpr', 'TPR.G16346' => 'tpr', 'TPR.G17678' => 'tpr', 'TPR.G37152' => 'tpr', 'TWI15G0007' => 'twi', 'TWI18G0368' => 'twi', 'TWI38G0122' => 'twi', 'TWI38G1874' => 'twi', 'TWI60G0991' => 'twi', 'unitig_22.g6223' => 'ugi', 'unitig_32.g11799' => 'ugi', 'unitig_62.g23769' => 'ugi', 'unitig_748.g8640' => 'ugi', 'vmacro03910' => 'vma', 'vmacro12436' => 'vma', 'vmacro16956' => 'vma', 'VMungo0251G0733' => 'vmu', 'VMungo0251G1695' => 'vmu', 'VMungo0331G1886' => 'vmu', 'VMungo1080G1378' => 'vmu', 'VMungo1127G1519' => 'vmu', 'VMungo1215G2673' => 'vmu', 'Zm00001eb024460' => 'zma', 'Zm00001eb043340' => 'zma', 'Zm00001eb338980' => 'zma' ) $gf_id = 'HOM05D001142' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001142' ) $data_identifier = 'HOM05D001142' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 7, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 6, 'camsi' => (int) 11, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 15, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 17, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 9, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 8, 'pco' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb338980' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1